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Targeted site integration in plants using a transposon system [Amplicon]

ABSTRACT: Targeted site integration in plants using a transposon system [Amplicon]

PROVIDER: PRJNA943234 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23803380.fastq.gz	Fastqsanger.gz
	SRR23803381.fastq.gz	Fastqsanger.gz
	SRR23803382.fastq.gz	Fastqsanger.gz
	SRR23803383.fastq.gz	Fastqsanger.gz
	SRR23803384.fastq.gz	Fastqsanger.gz

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Targeted site integration in plants using a transposon system

Project description:Targeted site integration in plants using a transposon system

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Targeted site integration in plants using a transposon system [insertion-seq]

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Targeted site integration in plants using a transposon system [Amplicon]

Project description:Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.

2024-05-03 | GSE227103 | GEO

Targeted site integration in plants using a transposon system

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-05-03 | GSE227105 | GEO

Targeted site integration in plants using a transposon system [insertion-seq]

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Integration of systemic signals in plants

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The Transposon Insertion site Profiling Chip (TIP-chip)

Project description:We have developed a microarray intended for use in finding all transposons in a region of interest. By selectively amplifying and hybridizing transposon flanking DNA to our array, we can localize all transposons in the region present on our TIP-chip, a dense tiling array. We have tested our technology in yeast and have been successful. Keywords: transposon insertion profiling, genomic DNA, yeast

2007-01-01 | GSE5646 | GEO

Transposon site hybridization (TraSH) screen in the lungs

Project description:We wanted to identify Francisella tularensis bacterial mutants that are negatively selected in vivo in the lungs of mice. Mice were infected with a Francisella transposon mutant library where each gene in the genome has been mutated via the insertion of a kanamycin resistance cassette with 2 outward facing T7 promoters. 2 days post infection, infected lungs were harvested and the bacteria present in the infected lungs were collected. Bacterial genomic DNA was isolated and subjected to an in vitro T7 transcription reaction, reverse transcribed and the resulting cDNA was hybridized to our Francisella microarray. Infection: The goal of the study was to identify Francisella genes that are negatively selected in the lungs of mice post infection with a Francisella transposon mutant library. Resulting bacterial cDNA was hybridized to the Francisella microarray.

2010-06-09 | GSE22231 | GEO

Integration site selection by the Bacteroides conjugative transposon CTnBST.

Project description:A newly discovered Bacteroides conjugative transposon (CTn), CTnBST, integrates more site specifically than two other well-studied CTns, the Bacteroides CTn CTnDOT and the enterococcal CTn Tn916. Moreover, the integrase of CTnBST, IntBST, had the C-terminal 6-amino-acid signature that is associated with the catalytic regions of members of the tyrosine recombinase family, most of which integrate site specifically. Also, in most of these integrases, all of the conserved amino acids are required for integration. In the case of IntBST, however, we found that changing three of the six conserved amino acids in the signature, one of which was the presumed catalytic tyrosine, resulted in a 1,000-fold decrease in integration frequency. Changes in the other amino acids had little or no effect. Thus, although the CTnBST integrase still seems to be a member of the tyrosine recombinase family, it clearly differs to some extent from other members of the family in its catalytic site. We also determined the sequence requirements for CTnBST integration in the 18-bp region where the crossover occurs preferentially during integration. We found that CTnBST integrates in this preferred site about one-half of the time but can also use other sites. A consensus sequence was tentatively derived by comparison of a few secondary sites: AATCTGNNAAAT. We report here that within the consensus region, no single base change affected the frequency of integration. However, 3 bp at one end of the consensus sequence (CTG) proved to be essential for integration into the preferred site. This sequence appeared to be at one end of a 7-bp crossover region, CTGNNAA. The other bases could vary without affecting either integration frequency or specificity. Thus, in contrast to well-studied site-specific recombinases which require homology throughout the crossover region, integration of CTnBST requires homology at one end of the crossover region but not at the other end.

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DNA sequences at integration sites in primary mammary tumors and lung metastases from a sleeping-beauty transposon-mediated mutagenesis screen on Rb-deficient background

Project description:This deposition describes DNA sequences at integration sites in primary tumors and lung metastases from a sleeping-beauty transposon-mediated mutagenesis screen on Rb-deficient background in the mammary gland in MMTV-Cre:Rbf/f:T2/Onc3a:R26lsl_SB11 and MMTV-Cre:Rbf/f:T2/Onc3b:R26lsl_SB11 female mice. In these mice, Rb floxed (Rbf/f) alleles and a SB11 transposase, knocked into the ROSA26 locus (R26lsl_SB11), are mobilized via MMTV-Cre. Two different transgenic transposon concatemers, T2/Onc3a and T2/Onc3b, containing 11 and 28 copies on chromosomes 9 and 12 were used so that local hoping in the respective chromosomes can be discarded. These mice developed large primary tumors and macroscopic lung metastases; biopsies from the primary tumors and entire lung metastases were used to extract DNA. The DNA was subjected to sonication, ligation-mediated PCR with 79 bar coded primers, followed by next-generation DNA sequencing. We identified Primary-specific and lung Metastasis-specific gene-centric Common Integration Sites (gCIS) as well as shared gCIS, observed in both primary mammary tumors and lung metastases. Using sequence analysis of integration sites, we were able to demonstrate in multiple cases clonal relationship between primary lesions and metastases. The metastatic gCIS form specific hubs that may be prioritized for targeted therapy. For details, see reference below.

2023-05-17 | GSE232167 | GEO

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